Entry to the school is by audition and assessment, based on musical ability and potential and regardless of personal circumstances. Scottish Government funding, up to 100%, is available through the statutory Aided Places scheme to assist with the cost of tuition and boarding fees. The school and St Mary's Cathedral also award bursaries. The school draws pupils from many different backgrounds, from all parts of Scotland and abroad. Boarding facilities are available at Coates Hall.
The school operates a large chamber orchestra, a Junior String Sinfonia and a Senior String Ensemble. Jazz and Traditional Scottish Music (including instruments like the clàrsach and bagpipes) feature in specialist ensembles and in Jazz and Scottish Music Days. Students perform regularly throughout Edinburgh and beyond. In addition to internal lunchtime concerts, students have also performed at the Queen's Hall, Edinburgh, Jam House, Kirks, Cathedral and the Royal Conservatoire of Scotland in Glasgow. Students have also been requested to play at many civic occasions including Royalty, the Scottish Parliament and other public events such as a NATO visit to Edinburgh.
In addition, students play regularly in external youth orchestras such as the Edinburgh Youth Orchestra, National Children’s Orchestra of Scotland, National Youth Orchestra of Scotland, National Children's Orchestra of Great Britain and the National Youth Orchestra of Great Britain and sing in the National Youth Choir of Scotland.
Students also have the opportunity to form their own bands such as the contemporary folk-fusion band Kilairum.
The school day is from 8.30am until 5pm (3.30 on Wednesdays and 4.30 on Fridays) - and there is no study leave. The School is regularly at or near the top of Scotland’s academic league tables. St Mary's Music School was named as Scottish Independent Secondary School of the Year in 2007 and its academic results are consistently excellent. The 2016 pass rate is 100% for National 4, Higher and A level exams, 94% for National 5 and 95% for Advanced Highers. A former Music Director, Nigel Murray, wrote in 1994 that the self-discipline acquired in the devotion to the mastery of an art as self-fulfilling as Music was bound to have a beneficial effect on the rest of the pupil's work and play. Murray continued that if he had a motto for St Mary's Music School it would be the words of the Italian pianist Ferruccio Busoni; "He who is only a musician is no musician".